January, 2021

Introducing: Jan Burnik

Today we talk to Jan Burnik, who is a PhD student working on protein crystallography in Prof. Eckhard Hofmann's group. He joined MiCon as a full-member immediately after the start of the graduate college in summer 2018.

What are you doing in the lab, Jan?

During my studies, I always wanted to work with enzymes that matter. That is why I’m working in the field of Hydrogenases ever since. The long-term hope is to contribute to a cleaner and greener future of our society.
My experimental focus is protein crystallography. The best phrase to describe this method might be ‘seeing is believing’. My students and I currently working on three [FeFe]-Hydrogenases. The first one’s a classic: HydA1 from Chlamydomonas reinhardtii, our model enzyme. Furthermore, we are investigating the two less considered enzymes CpII and CpIII of the soil bug Clostridium pasteurianum. We want to find out what the structural differences are between the three hydrogenases and how these contribute to the different catalytic properties of the enzymes. My second project is some kind of ‘heart project’: I refuse to believe that it is impossible to solve the structure of holo-HydA1. If the native protein does not crystallize, we simply have to create a solution that works. Therefore, I strengthen and stabilize the holoform covalently and non-covalently before attempting to crystallize these improved variants.

What do you like about the RTG?

Regarding the covalent stabilisation of protein variants, I got some ideas when I asked one of our PI’s, Dirk Tischler, for help. That’s probably the best part of the RTG. As we (the PhD students) meet frequently with all PI's during MiCon events and in between, the exchange of ideas and solutions to individual, and sometimes very specific research problems is high. Also, it often helps to share your own misery with your fellow researchers, and often you get a different and useful perspective on your own project, which helps you solve your problems, and vice versa.

January, 2021

Introducing: Anna Frank

Anna Frank has been on board with the RTG MiCon since its inception in 2018 and is part of the management team. She works in the group of Prof. Marc Nowaczyk on the elucidation of molecular mechanisms of photosynthesis.

What are you doing in the lab, Anna?

In my project I am seeking for a way to utilize natural photosynthesis to drive desired reactions – just by the power of (sun)light. Wiring enzymatic catalysts to the photosynthetic machinery of cyanobacteria allows a production of e.g. biofuels or fine chemicals in an environmentally friendly process, without the need for harmful chemical components, high temperatures or pressure. My particular focus is on enzymes of the Cytochrome P450 family that convert naturally occurring fatty acids in cyanobacteria into precursor molecules that can be used for the production of fine chemicals, pharmaceuticals and advanced materials. Additionally, the coupling of the cyanobacterial-own hydrogenase to Photosystem I, done in the lab of our collaboration partner Dr. Gutekunst at the University of Kiel, is promising to allow light-driven production of biohydrogen as a clean biofuel. For the project, we work together with several groups from Germany, Israel and Japan and are happy to share our progress at the Cyano 2019, Biohybrid 2020 and other conferences to come.

What's the best part about being in a collaborative RTG?

I am very fortunate to have benefited from close collaboration with various groups within MiCon. Especially the group of Prof. Dr. Tischler supports my work by providing the Cyt P450 enzymes that are a key component of my project and by enabling the regular use of their gas chromatography facilities for sample analysis. Prof. Hofmann’s group provided us with a quick and easy technique for cell disruption of cyanobacteria via a microfluidizer.
My advice: Take the opportunity to discuss your problems in a large audience with members of different groups. The combined experience of interdisciplinary groups is immense and chances are very high, that you will get surprising ideas and help offers from others that you would have never come to by yourself.

December, 2020

Introducing: Jan Plewka-Mandelkow

Jan Plewka-Mandelkow is a PhD student in the group of Professor Dr. Ute Krämer, Chair of Molecular Genetics and Physiology of Plants. He did his Master thesis at the University of Cologne in cooperation with the Max Planck Institute for Plant Breeding Research before joining the Ruhr University at the beginning of 2020.

What are you doing in the lab, Jan?

I am a plant scientist focusing on plant-microbe-interactions. To be more specific, I explore bacteria living on or inside plant leaves. It is well-known that colonizing microbiota have a significant influence on their host’s health. Consequently, plant hosts can shape their microbiota structure and behavior by the production and accumulation of secondary metabolites, for example coumarins, glucosinolates, or camalexin. This was demonstrated in the well-recognized model organism Arabidopsis thaliana. Another possible mechanism to shape the microbiota in a leaf might be the accumulation or depletion of trace elements in the plant apoplast. In my first project, I am investigating the variation of metal tolerances among bacterial isolates of the phyllosphere of A. thaliana. In a second project, I isolated around 300 zinc- and cadmium-tolerant endophytic bacteria from the metal hyperaccumulator Arabidopsis halleri, which is able to grow on soils containing extremely high metal concentrations. I will use these strains as a model system to explore plant-microbe interactions in metal hyperaccumulators. Additionally, I am comparing the microbiota from wild type plants and mutant lines impaired in zinc and cadmium hyperaccumulation and from plants vastly contrasting in leaf metal accumulation in the field.

What is your personal benefit from participating in an interdisciplinary graduate program?

I profited a lot from the networking opportunities created by the RTG. I already got several helpful bits of advice from scientists from outside my research group. I also got help, in an efficient and uncomplicated manner, from other groups that pushed my projects important steps forward. Moreover, I received travel funding to visit the group of Professor Dr. Julia Vorholt at the ETH Zürich, from where I transferred the A. thaliana phyllosphere collection to our institute and learnt how to work with it. For the next generations of fellows or associated scientists, I highly recommend using these networking opportunities for their own projects to improve their science. I am still in my first year, so I am looking forward to the future opportunities organized by and with the RTG.

November, 2020

Introducing: Anna Christina Lienkamp

Anna Christina Lienkamp is a MiCon member of the first hour and works in the group of Professor Dr. Dirk Tischler on the interface between microbiology, biotechnology and biochemistry. She started her PhD work back in July 2018 working on new enzymes and pathways in Actinobacteria.

What are you doing in the lab, Anna?

My research project is about the glutathione-dependent degradation of xenobiotics in actinobacterial pathways. Actinobacteria, which can grow on rare and mostly toxic carbon sources like isoprene or styrene, gain this unique ability through specific sets of enzymes. I am working on some of these enzymes regarding their characteristics and role in the native degradation pathways. It has been shown that the actinobacterium Gordonia rubripertincta converts a styrene derivative to ibuprofen, which is just one example of many for a potential biotechnological application. Generally, the production of substituted phenylacetic acids in the course of this pathway can serve a broad range of industrial applications for not only several drugs but also flavours and fragrances. My project combines protein biochemistry with analytical methods and requires a wide set of techniques and devices, which keeps it challenging and broadens the development of my scientific skills. My favourite part so far is the identification of reaction products by liquid chromatography mass spectrometry and the most exciting part is to currently write my first publication about the recent results.

How did you personally benefit from being part of this RTG? Do you have any advice for the next generation of fellows?

Being part of the MiCon RTG is an experience I would highly recommend to my fellow students. The biggest scientific benefit is the permanent exchange of knowledge and techniques. Outstanding herein is the diversity of scientific backgrounds by the members but a shared common basic knowledge and thematic proximity of the overall topics. This helps to critically examine each other’s research projects by giving and receiving many constructive advices and thus more solutions to potential problems. Additionally, we complement and help each other with sets of devices, protocols and techniques giving more options for everyone’s research. Personally, I value the scientific and personal exchange about doing a PhD and being part of an interdisciplinary and international scientific community. Sharing similar experiences and enjoying the social activities offered definitely adds up to the quality of my PhD and helped me a lot in being a more professional researcher. My advice for the new students to come would be to use the benefit of networking because it raises the quality of overall education and science in general.


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